From: daniel aguayo (bioquimico_at_gmail.com)
Date: Thu Oct 15 2009 - 19:46:12 CDT
Hi All
I have to give my thanks to all the people who answer questions on the
list. Because they help my a lot to get a better understanding of MD and
other aspects of this fields.
I answer too when I have the knowledge to do it.
But most of the time, I found the answer to my questions on the old posts.
At the end, just TKs to all Samaritans out there.
Cheers
DAV
On Thu, Oct 15, 2009 at 9:15 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, 2009-10-15 at 11:22 -0400, Roman Petrenko wrote:
> > Guys, thanks for replies,
> >
> > 1) yes i wrap all
> >
> > 2) why 2 fs is an aggressive timestep. i thought the larger the system
> > the more applicable is this timestep, because we don't care about high
> > frequency motion.
>
> first off, the physics of the system and the integrator don't
> care about what you care about. the larger the system, the larger
> the possible fluctuations (including velocities) within the system.
>
> what i suspect is that you may just accidentally have had some
> very large force(s) on some atom(s) and that then the integrator
> broke down. since you increased the additional force due to the
> external field by a factor of 10, that may have become a significant
> contribution and just enough to bring the system over the top.
>
> of course, this is just a speculation based on my experiences
> with simulations on driving electrolytes through nanopores
> with (strong) external fields some 10+ years back. i would
> assume that a membrane protein system is much more sensitive
> than the crude models that we were able to run in the (good?)
> old times. ;-)
>
> if you don't care about fast motions, you could fiddle with the
> settings of the langevin thermostat, i.e. add more friction
> to make fast movements slower and stabilize a larger time step.
>
>
> > 3) center of mass drifts a _little bit_; is it that bad taking into
> > account that box expands eventually to 5000 A and center of mass moved
> > mere 170 A; here is center of mass of the system from complete
> > trajectory:
>
> as soon as the system expands significantly your results are bogus,
> so it is useless to discuss the 170A (which would be horrible), but
> the rest looks not too bad. when working with external fields, the
> COM drift is always an iffy issue and has to be monitored carefully,
> since there is always a chance that you become a victim of the
> "flying icecube syndrom", i.e. the total system starts to drift,
> and then due to the impact of the termostat your system effectively
> cools down. this is, obviously, correlated with the strength of the
> external field. in a "normal" system without an external field and
> if it is reasonably well equilibrated system, the langevin thermostat
> in NAMD should take care that the drift, once removed, does not
> build up again.
>
> [...]
>
> > 4) I wonder why people who did DNA translocation don't reply. Am i the
> > only one who set up simulation system incorrectly? :)
>
> i don't think you are the only one and i believe this is a general
> problem. i've been complaining about this on various mailing lists
> and many times. my estimate is that on every person that asks a
> question on a mailing lists, there are at least 100 people that
> are subscribed and should have posted the same question and did
> dare to, and for people answering the ratio is even worse.
>
> i am still trying to make sense of this scenario. i feel a lot of
> it is due to how the way we do research has been changing of the
> last 10-15 years. it is much easier to get started to do simulations
> with packages like NAMD and all the documentation and tutorial
> material around, so people feel more often that they are not expert
> enough to answer, but also there is the problem of people that
> tend to rather post a (too) trivial question instead of sitting
> for five minutes and thinking about it. so if this kind of question
> gets "shot down", it seems to intimidate those, that actually do
> have good questions and _should_ ask.
>
> personally, i feel a strong obligation to help people with what
> i know, when people from the same community have helped me before
> (my boss repeatedly called me "a good samaritan" because of that),
> but then i also get the impression (and have been told so by some
> people) that (too) many people view answering (trivial) questions
> on mailing lists a waste of time (as they feel there is nothing in
> it for them). in my personal experience, there is a lot to be gained
> from sharing your knowledge, as it helps confirming your understanding
> of the principles and one always has the option to start with
> answering simple questions and then move on. i learned a lot about
> many tools and methods just through this, _much_ more than i would
> have ever learned by just "lurking". it is a pity that there are
> no simple ways to reward people when they more actively participate
> in forums like this... (i know that intel for example has a point
> system, where people that answer often and correct in their support
> forums, get a higher ranking and - depending on the ranking - some
> benefits, but then again, that is a much larger community and they
> have loads of cash).
>
> cheers,
> axel.
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
-- saludos desde el fin del mundo
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